Regenerate parsers with unified runtime

Author: GlassOfWhiskey

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -12,6 +12,7 @@
 
 from ruamel import yaml
 from schema_salad.metaschema import ArraySchema
+from schema_salad.runtime import LoadingOptions, save
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 
@@ -42,7 +43,7 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
             stdout_path = process.stdout
             if not stdout_path:
                 stdout_path = hashlib.sha1(  # nosec
-                    json_dumps(cwl.save(process)).encode("utf-8")
+                    json_dumps(save(process)).encode("utf-8")
                 ).hexdigest()
                 result.stdout = stdout_path
             result.outputs[index].type_ = "File"
@@ -1219,7 +1220,7 @@ def process_level_reqs(
 
 
 def add_input_to_process(
-    process: cwl.Process, name: str, inptype: Any, loadingOptions: cwl.LoadingOptions
+    process: cwl.Process, name: str, inptype: Any, loadingOptions: LoadingOptions
 ) -> None:
     """Add a new InputParameter to the given CommandLineTool."""
     if isinstance(process, cwl.CommandLineTool):

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -12,6 +12,7 @@
 
 from ruamel import yaml
 from schema_salad.metaschema import ArraySchema
+from schema_salad.runtime import LoadingOptions, save
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 
@@ -42,7 +43,7 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
             stdout_path = process.stdout
             if not stdout_path:
                 stdout_path = hashlib.sha1(  # nosec
-                    json_dumps(cwl.save(process)).encode("utf-8")
+                    json_dumps(save(process)).encode("utf-8")
                 ).hexdigest()
                 result.stdout = stdout_path
             result.outputs[index].type_ = "File"
@@ -1221,7 +1222,7 @@ def process_level_reqs(
 
 
 def add_input_to_process(
-    process: cwl.Process, name: str, inptype: Any, loadingOptions: cwl.LoadingOptions
+    process: cwl.Process, name: str, inptype: Any, loadingOptions: LoadingOptions
 ) -> None:
     """Add a new InputParameter to the given CommandLineTool."""
     if isinstance(process, cwl.CommandLineTool):

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -12,6 +12,7 @@
 
 from ruamel import yaml
 from schema_salad.metaschema import ArraySchema
+from schema_salad.runtime import LoadingOptions, save
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 
@@ -41,7 +42,7 @@ def expand_stream_shortcuts(process: cwl.CommandLineTool) -> cwl.CommandLineTool
             stdout_path = process.stdout
             if not stdout_path:
                 stdout_path = hashlib.sha1(  # nosec
-                    json_dumps(cwl.save(process)).encode("utf-8")
+                    json_dumps(save(process)).encode("utf-8")
                 ).hexdigest()
                 result.stdout = stdout_path
             result.outputs[index].type_ = "File"
@@ -1324,7 +1325,7 @@ def process_level_reqs(
 
 
 def add_input_to_process(
-    process: cwl.Process, name: str, inptype: Any, loadingOptions: cwl.LoadingOptions
+    process: cwl.Process, name: str, inptype: Any, loadingOptions: LoadingOptions
 ) -> None:
     """Add a new InputParameter to the given CommandLineTool."""
     if isinstance(process, cwl.CommandLineTool):

cwl_utils/expression_refactor.py

@@ -13,6 +13,7 @@
 
 from ruamel.yaml.main import YAML
 from ruamel.yaml.scalarstring import walk_tree
+from schema_salad.runtime import save
 
 from cwl_utils import (
     cwl_v1_0_expression_refactor,
@@ -111,15 +112,12 @@ def refactor(args: argparse.Namespace) -> int:
                 traverse: Callable[[Any, bool, bool, bool, bool], tuple[Any, bool]] = (
                     cwl_v1_0_expression_refactor.traverse
                 )
-                save: saveCWL = cwl_v1_0.save
             case "v1.1":
                 top = cwl_v1_1.load_document_by_yaml(result, uri)
                 traverse = cwl_v1_1_expression_refactor.traverse
-                save = cwl_v1_1.save
             case "v1.2":
                 top = cwl_v1_2.load_document_by_yaml(result, uri)
                 traverse = cwl_v1_2_expression_refactor.traverse
-                save = cwl_v1_2.save
             case _:
                 _logger.error(
                     "Sorry, %s is not a supported CWL version by this tool.",

cwl_utils/normalizer.py

@@ -12,12 +12,13 @@
 
 from cwlupgrader import main as cwlupgrader
 from ruamel import yaml
+from schema_salad.runtime import save
 from schema_salad.sourceline import add_lc_filename
 
 from cwl_utils import cwl_v1_2_expression_refactor
 from cwl_utils.loghandler import _logger as _cwlutilslogger
 from cwl_utils.pack import pack
-from cwl_utils.parser.cwl_v1_2 import load_document_by_yaml, save
+from cwl_utils.parser.cwl_v1_2 import load_document_by_yaml
 
 _logger = logging.getLogger("cwl-normalizer")  # pylint: disable=invalid-name
 defaultStreamHandler = logging.StreamHandler()  # pylint: disable=invalid-name

cwl_utils/parser/__init__.py

@@ -4,10 +4,11 @@
 from abc import ABC
 from collections.abc import MutableMapping, MutableSequence
 from pathlib import Path
-from typing import Any, Optional, TypeAlias, cast
+from typing import Any, TypeAlias, cast
 from urllib.parse import unquote_plus, urlparse
 
 import schema_salad.metaschema
+import schema_salad.runtime
 from schema_salad.exceptions import ValidationException
 from schema_salad.utils import yaml_no_ts
 
@@ -19,11 +20,9 @@ class NoType(ABC):
     pass
 
 
-LoadingOptions: TypeAlias = (
-    cwl_v1_0.LoadingOptions | cwl_v1_1.LoadingOptions | cwl_v1_2.LoadingOptions
-)
+LoadingOptions: TypeAlias = schema_salad.runtime.LoadingOptions
 """Type union for a CWL v1.x LoadingOptions object."""
-Saveable: TypeAlias = cwl_v1_0.Saveable | cwl_v1_1.Saveable | cwl_v1_2.Saveable
+Saveable: TypeAlias = schema_salad.runtime.Saveable
 """Type union for a CWL v1.x Saveable object."""
 InputParameter: TypeAlias = (
     cwl_v1_0.InputParameter | cwl_v1_1.InputParameter | cwl_v1_2.InputParameter
@@ -235,7 +234,7 @@ class NoType(ABC):
     | cwl_v1_2.WorkflowStepInput
 )
 """Type Union for a CWL v1.x LoadContents object."""
-_Loader: TypeAlias = cwl_v1_0._Loader | cwl_v1_1._Loader | cwl_v1_2._Loader
+_Loader: TypeAlias = schema_salad.runtime._Loader
 """Type union for a CWL v1.x _Loader."""
 
 
@@ -286,53 +285,16 @@ def load_document_by_uri(
         base_uri = path.resolve().parent.as_uri()
         id_ = path.resolve().name.split("#")[1] if "#" in path.resolve().name else None
 
-    match loadingOptions:
-        case cwl_v1_0.LoadingOptions():
-            loadingOptions = cwl_v1_0.LoadingOptions(
-                fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
-            )
-            return load_document_by_string(
-                loadingOptions.fetcher.fetch_text(real_uri),
-                real_uri,
-                loadingOptions,
-                id_,
-                load_all,
-            )
-        case cwl_v1_1.LoadingOptions():
-            loadingOptions = cwl_v1_1.LoadingOptions(
-                fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
-            )
-            return load_document_by_string(
-                loadingOptions.fetcher.fetch_text(real_uri),
-                real_uri,
-                loadingOptions,
-                id_,
-                load_all,
-            )
-        case cwl_v1_2.LoadingOptions():
-            loadingOptions = cwl_v1_2.LoadingOptions(
-                fileuri=real_uri, baseuri=base_uri, copyfrom=loadingOptions
-            )
-            return load_document_by_string(
-                loadingOptions.fetcher.fetch_text(real_uri),
-                real_uri,
-                loadingOptions,
-                id_,
-                load_all,
-            )
-        case None:
-            loadingOptions = cwl_v1_2.LoadingOptions(fileuri=real_uri, baseuri=base_uri)
-            return load_document_by_string(
-                loadingOptions.fetcher.fetch_text(real_uri),
-                real_uri,
-                None,
-                id_,
-                load_all,
-            )
-        case _:
-            raise ValidationException(
-                f"Unsupported loadingOptions type: {type(loadingOptions)}"
-            )
+    if loadingOptions is None:
+        loadingOptions = LoadingOptions(fileuri=real_uri, baseuri=base_uri)
+
+    return load_document_by_string(
+        loadingOptions.fetcher.fetch_text(real_uri),
+        real_uri,
+        loadingOptions,
+        id_,
+        load_all,
+    )
 
 
 def load_document(
@@ -344,7 +306,7 @@ def load_document(
 ) -> Any:
     """Load a CWL object from a serialized YAML string or a YAML object."""
     if baseuri is None:
-        baseuri = cwl_v1_0.file_uri(str(Path.cwd())) + "/"
+        baseuri = schema_salad.runtime.file_uri(str(Path.cwd())) + "/"
     if isinstance(doc, str):
         return load_document_by_string(doc, baseuri, loadingOptions, id_)
     return load_document_by_yaml(doc, baseuri, loadingOptions, id_, load_all)
@@ -376,17 +338,11 @@ def load_document_by_yaml(
         yaml["cwlVersion"] = version
     match version:
         case "v1.0":
-            result = cwl_v1_0.load_document_by_yaml(
-                yaml, uri, cast(Optional[cwl_v1_0.LoadingOptions], loadingOptions)
-            )
+            result = cwl_v1_0.load_document_by_yaml(yaml, uri, loadingOptions)
         case "v1.1":
-            result = cwl_v1_1.load_document_by_yaml(
-                yaml, uri, cast(Optional[cwl_v1_1.LoadingOptions], loadingOptions)
-            )
+            result = cwl_v1_1.load_document_by_yaml(yaml, uri, loadingOptions)
         case "v1.2":
-            result = cwl_v1_2.load_document_by_yaml(
-                yaml, uri, cast(Optional[cwl_v1_2.LoadingOptions], loadingOptions)
-            )
+            result = cwl_v1_2.load_document_by_yaml(yaml, uri, loadingOptions)
         case None:
             raise ValidationException("could not get the cwlVersion")
         case _:
@@ -412,7 +368,7 @@ def save(
 ) -> Any:
     """Convert a CWL Python object into a JSON/YAML serializable object."""
     match val:
-        case cwl_v1_0.Saveable() | cwl_v1_1.Saveable() | cwl_v1_2.Saveable():
+        case Saveable():
             return val.save(top=top, base_url=base_url, relative_uris=relative_uris)
         case MutableSequence():
             lst = [